We use GitHub for version control on our software. All members of the lab have their own pages, and there are also common repos for things we work on together. Here are links to our repositories where you can find what we worked on before, and what we’re working on now!
ReadMapper is based on R code that was written to analyze our inhouse data. The code has been modified to make it user friendly and allow other people, who are not as versed in the R language, to be able to map sequencing reads to a nucleotide backbone, and create publication quality figures. In our project we were mapping translatome data to the genome of the phage Lambda (this is what the included sample data is), as well as the currently annotated gene open reading frames. Which looks just like the figure below.
Yet again, analysis of a metagenomic sample shows that crAssphage is the most abundant phage anywhere. It also shows what a dis-service NCBI did to science by deleting the crAssphage record. We used meta-spades to reconstruct the entire crAssphage genome from someone else’s data set, but in their paper, the largest contig was ~3 kb. This analysis suggests that crAssphage is present in ulcerative colitis samples but the abundance goes down after treatment!